[Chimera-users] RMSD fit of an object to atom

Tom Goddard goddard at cgl.ucsf.edu
Wed Mar 7 12:13:54 PST 2007

Hi Eric,

  Chimera does not have a convenient way to move a marker placed with 
the path tracer tool to the highest local value in a map.  A tricky way 
to do it is to use the Fit Model in Map tool (under menu Tools / Volume 
Data).  If you have just one marker in a marker set you can select that 
marker and move it to the local maximum with the Fit button.  If there 
are multiple markers in your marker set then all of them are moved 
rigidly as a group so this trick does not work so well.  It would be 
easy to add a keyboard shortcut that would move single markers or atoms 
to the local density maximum.

  I didn't understand your explanation of why 4 points are needed for an 
alignment with the match command.  It looks like only 3 are needed for a 
unique match.  In your example with points ABC and DEF you suggested 
that the match could either pair A with D, B with E, and C with F or it 
could pair A with F, B with E, C with D.  But the match command 
specifies the desired pairing so only one of those is possible for any 
match command invocation.


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